Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SearchIO::blast_pull - A parser for BLAST output

SYNOPSIS

           # do not use this class directly it is available through Bio::SearchIO
           use Bio::SearchIO;
           my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                      -file   => 't/data/new_blastn.txt');
           while (my $result = $in->next_result) {
               # this is a Bio::Search::Result::BlastPullResult object
               print "Results for ", $result->query_name(), "\n";
               while (my $hit = $result->next_hit) {
                   print $hit->name(), "\n";
                   while (my $hsp = $hit->next_hsp) {
                       print "length is ", $hsp->length(), "\n";
                   }
               }
           }

DESCRIPTION

       This object implements a pull-parser for BLAST output. It is fast since it only does work
       on request (hence 'pull').

       Currently only NCBI BLASTN and BLASTP are supported.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::SearchIO::blast_pull->new();
        Function: Builds a new Bio::SearchIO::blast_pull object
        Returns : Bio::SearchIO::blast_pull
        Args    : -fh/-file => BLAST output filename
                  -format   => 'blast_pull'
                  -evalue   => float or scientific notation number to be used
                               as an evalue cutoff for hits
                  -score    => integer or scientific notation number to be used
                               as a score value cutoff for hits
                  -piped_behaviour => 'temp_file'|'memory'|'sequential_read'

                  -piped_behaviour defines what the parser should do if the input is
                   an unseekable filehandle (eg. piped input), see
                   Bio::PullParserI::chunk for details. Default is 'memory'.

   next_result
        Title   : next_result
        Usage   : my $hit = $searchio->next_result;
        Function: Returns the next Result from a search
        Returns : Bio::Search::Result::ResultI object
        Args    : none

   result_count
        Title   : result_count
        Usage   : my $count = $searchio->result_count
        Function: Returns the number of results we have processed.
        Returns : integer
        Args    : none

   rewind
        Title   : rewind
        Usage   : $searchio->rewind;
        Function: Allow one to reset the Result iterator to the beginning, so that
                  next_result() will subsequently return the first result and so on.

                  NB: result objects are not cached, so you will get new result objects
                  each time you rewind. Also, note that result_count() counts the
                  number of times you have called next_result(), so will not be able
                  tell you how many results there were in the file if you use rewind().

        Returns : n/a
        Args    : none